The association between hepatitis b virus hbv mutations and. Use with snapgene software or the free viewer to visualize additional data and align other sequences. Hbv infection and epidemic in asia appear more severe. Highthroughput sequence data for neolithic and medieval virus genomes reveal complex evolution of hepatitis b. Amino acid sequences coded for by the s, c, p and x genes.
Hbv is a major health problem worldwide with more than 350 million individuals being chronically infected. Hbv dna was extracted from serum specimens by using a modification of the master pure procedure epicentre technologies, madison, wi in which 50. Universal primers for hbv genome dna amplification across. Sep 24, 2007 the highly heterogenic characteristic of viruses is the major obstacle to efficient dna amplification. The new genome sequence was obtained by first mapping reads to a reference sarscov2 genome using bwamem 0. Subcloning was done in three parts of hbv dna from patients fh1 and ah1. Each hepatitis b virus hbv genotype and subgenotype is associated with a particular geographic distribution, ethnicity, and anthropological history. Our group includes molecular biologists, sequence analysts, computer technicians, postdocs and graduate research assistants. Here, we present the first characterization and complete genome sequence of a strain belonging to genotype e in mexico, obtained from a foreign carrier with chronic infection.
Although the findings of the study is limited and like a genome announcement, it signifies to be documented. Similar in public databases, sequence number from mainland china ranks the highest, and then in order are china hong kong, japan, africa, europe, and north america. More than 260 million people worldwide have chronic hbv infection, which causes 0. Hbx interacts with chromatin modifying enzymes and transcription factors to modulate histone posttranslational modifications and to regulate viral cccdna transcription and cellular gene expression. Idea shamelessly stolen from mick watsons kraken downloader scripts that can also be found in micks github repo. We analyzed hbvlike sequences from three chimpanzees pan troglodytes that were most likely infected during their life in africa in the wild. The current practice of using overlapping conserved primer sets to amplify a complete hbv genome in a clinical. The aim of this study was to characterize the hbv genotypes circulating in quibdo, the largest afrodescendant community in colombia. Illumina and nanopore methods for whole genome sequencing. The conventional practice of using a single set of primers to amplify a nearcomplete hbv genome is hampered by its low analytical sensitivity. Here by conducting highthroughput viral integration detection and rna. The taxonomic rank which gets assigned is based on availability of reference genomes in refseq, and is mostly at species level.
Maximum likelihood trees of fulllength hbv sequences from sample 31 sequenced by nanopore. Locate the directory for your organism of interest. If a mutation caused a sequence mismatched in the primer or probe of a commercial dna quantification kit, this would lead to an. Cloning and sequencing of hbv dna has provided evidence that the gene coding for hbv env proteins has the capacity to code for proteins larger than the 226 amino acid chain of p25 tiollais et al. Machinelearning based patient classification using. Search interface retrieves hiv and siv sequences, which can then be aligned and used to build trees. Here, we report the complete nucleotide sequence of a precoredefective hbv genotype d2 strain isolated in bangladesh. The complete nucleotide sequences of the dna of three hepatitis b virus hbv genomes of subtype adw, cloned from plasma samples of asymptomatic carriers living in the mainland and okinawa prefecture of japan and indonesia were determined. The combination of double and singlestranded dna in a single molecule can cause. Implications for an origin of hbv1 kazuaki takahashi, betsy brotman, sadakazu usuda, shunji mishiro,2 and alfred m.
Hepatitis b virus hbv infects the liver and is a key risk factor for hepatocellular carcinoma. Neolithic and medieval virus genomes reveal complex evolution. The phylogenetic tree was constructed with the data from these 38 isolates. Overview of hbv whole genome data in public repositories and the. Fullgenome sequence analyses of hepatitis b virus hbv. Complete genome sequence of the who international standard. Our previous study showed the novel hbv subgenotypes c6 hbv c6 and d6 hbv d6, based on the s gene sequences of isolates in papua, indonesia. The mutations defined as differences between the submitted sequence and the consensus reference sequence are used as query parameters for interrogating a local hbv rt drug resistance database hbvrt db to retrieve the prevalence of each mutation. One was fragment c nt 11258, amplified using primers ss1 and ss2, the second was fragment d nt 2459248, amplified using primers sp6 and as3 and the last was fragment e nt 991946, amplified using primers b3 and b2. Overview of hbv whole genome data in public repositories and. Hepatitis b virus hbv infection results in different clinical presentation due to different levels of immune response. May 10, 2018 the two neolithic hbv genomes clustered phylogenetically with, but distinctly from, african nonhuman primate hbv sequences, and the medieval hbv clustered with contemporary hbv d4 genome sequences. Complete genome sequences of hepatitis b virus from north. Complete genome sequence of the who international standard for.
The world health organization who international standard is for hepatitis b virus hbv dna for use in nucleic acid amplification assays was characterized by determining the complete genome sequence, which was assigned genotype a. Aiming to identify genes and noncoding rnas ncrnas directly. The genome was 3215 nucleotides long, and differed in dna sequence by 10% from that of subtypes adw or ayw, but by only 2% from that of subtype adr. The underlying mechanism of hbsagnegative hepatitis b virus hbv infection is notoriously. Complete genome sequence of hepatitis b virus hbv from a patient with fulminant hepatitis without precore and core promoter mutations. If the match length on both hbv genome reference and human genome reference for one peassembled read was larger than 30 bp, the peassembled read alignment result was reported to detect a precise breakpoint. Taking advantage of the large number of virus dna sequences in public databases to select conserved sites for primer design is an optimal way to tackle the difficulties in virus genome amplification. Forty treatmentnaive hbv infected patients were enrolled, including 10 cases of acute hepatitis b ahb, 9 cases of.
Nucleotide sequence variation in the genome has been used to classify hbv into different genotypes a to j 3, 4. Genomic and oncogenic preference of hbv integration in. The substitution rate is surprisingly high for a dna virus, but lower than that of other reverse transcribing organisms. Tools for working with sequences lists all our online tools, organized by function. Complete genome sequence of hepatitis b virus genotype e. Globally, more than 2 billion people have been infected by hbv 2,3 and, according to the world health organization who approximately 257 million were living with hbv in 2017. Citeseerx nucleotide sequence of a cloned hepatitis b virus. Hepatitis b virus infection is currently a global public health problem.
All three comprised 3215 bp and differed in sequence by only 3. Organization of overlapping open reading frames and approximate location of singlestranded portion of plus strand are indicated. This has additional annotation, for use with noncommercial sequence browsers e. Identification of hbv genotype and consensus sequences coverage across the genome results nanopore data figure 8. It is strongly recommended that you also download the original genbank file if you want to obtain a more complete picture of the ebv coding regions. Chronic infection is associated with an increased risk to develop severe liver. An efficient method to detect hbv integration using. Annotation, comparison, detection and visualization of. Overview of hbv whole genome data in public repositories. Neolithic and medieval virus genomes reveal complex. Although the diagnosis of acute and chronic hbv infection is usually made by serologic methods, detection and. Importantly, the authenticity of these hbv was also confirmed by the detection of a peptide of hbv core protein from two of the samples.
The hbv genome is also highlighted, showing the relevance of the overlap between the polymerase and envelope, so that mutations in one reading frame can affect the other. For successful hbv genome reconstruction, we mapped all metagenomic sequences to 16 hbv reference genomes eight human genotypes ah and 8 nhps from africa and asia that are representative of the current hbv strain diversity supplementary file 6. To construct hbvspecific grnas, we searched for a potential 20base target sequence on the genome of the genotype a hbvexpression vector paavhbv1. Deep sequencing of full length hepatitis b virus hbv. Nucleotide sequence of the hepatitis b virus genome. Complete genome sequence of a 2019 novel coronavirus sars.
Sequence variations of fulllength hepatitis b virus. Diagnosis of acute or chronic hepatitis b virus hbv infection is based on the presence of hbv serologic markers such as hepatitis b surface antigen hbsag and hepatitis b core igm antibody antihbc igm, or the presence of hbv dna detected by molecular assays. Association of hbv genome sequences with neighboring countries. The viral genomes resource is a collection of viral genomic sequences that is a part of the entrez genomes, which provides curated sequence data and annotations of complete genomes to. In colombia, our group reported recently the presence of subgenotypes f3, a2 and genotype g in bogota. Hepatitis b virus hbv can integrate into the human genome, contributing to genomic instability and hepatocarcinogenesis.
Hbv genome is optimized, being circular and encoding four overlapping reading frames. Hepatitis b virus hbv phylogenetic analysis was completed with reference strains ai as previously described, and hbv escape and resistance mutations were evaluated using geno2pheno hbv 2. Full genome sequences of hbv were performed in 38 patients with chronic hbv infection 11, 11, and 16 patients with hbv genotypes a, d, and c, respectively. Sitespecific rna bindding by a hepatitis b virus reverse transcriptase initiates two reactions. Dna, we analysed the sequences of the conserved region of the surface gene nucleotide nt 3055, representing 6. An hbv recombinant strain subgenotype f3a1 was found for the first time. Hbv has an unusual, circular, partially doublestranded ds dna genome of approximately 3. However, hbv is a dna virus with high levels of genetic variation, and drugresistant mutations have emerged with the use of antiviral drugs. Complete genome sequence of hepatitis b virus hbv from a. This information will aid the design, development, and evaluation of hbv dna amplification assays.
The virus tool assigns taxonomic names to sequences from eukaryotic viruses and phages. Nucleotide sequence of a cloned hepatitis b virus genome. Hepatitis b virus hbv genomic mutations affect viral replication, disease progression, and diagnostic and vaccination efficiency. A short cisacting sequence is required for hepatitis b virus pregome encapsidation and sufficient for packaging of foreign rna. The burden of chronic liver disease caused by hepatitis b virus hbv is increasingly detected at present 1. Hepatitis b virus hbv remains a major public health problem worldwide. Regulation of the hepatitis b virus replication and gene. Pdf comparative analysis of hepatitis b virus genome. To circumvent this problem, we modeled the hbv by duplicating the sequence of each reference genome from. Our study aimed to characterize hbv fulllength genome quasispecies qs in patients with different phases of infection to better understand its pathogenesis. Distinct hepatitis b virus dynamics in the immunotolerant and early immunoclearance phases. The complete nucleotide sequence of hepatitis b virus genome subtype ayw cloned in escherichia coli has been determined using the maxam and gilbert method and. May 10, 2018 consensus sequence of the petersberg hbv genome.
Analysis of the complete genome of hepatitis b virus. Nov 29, 2019 download one protein sequence per gene. Hepatitis b is caused by the hepatitis b virus hbv, an enveloped virus containing a partially double stranded, circular dna genome, and classified within the family hepadnavirus. Identification of hepatitis b virus indigenous to chimpanzees. Some script to download bacterial and fungal genomes from ncbi after they restructured their ftp a while ago. Complete genome sequence of a precoredefective hepatitis. Hbv causes hepatitis b, a serious and common infectious disease of the liver. The cobas hbv is a fdaapproved in vitro nucleic acid amplification test for the quantification of hepatitis b virus hbv dna in human serum, using the using the cobas 6800 or 8800 instrument for automated viral nucleic acid extraction silicabased capture technique, purification, amplification, and detection of the viral nucleic acid target. Hepatitis b virus subtype adw2, genotype a, complete genome. Hepatitis b virus hbv infection is one of the most prevalent viral infections in humans and represents a serious public health problem.
Pdf complete genome sequence and phylogenetic relatedness. The number of hepatitis b virus hbv whole genomic sequences in public nucleotide databases genbank, embl, and ddbj had reached 866 by january 1, 2007. Hepatitis b virus hbv is a unique, tiny, partially doublestranded, reversetranscribing dna virus with proteins encoded by multiple overlapping reading frames. Mandart, e, fitoussi, f, tiollais, p and charnay, p. Hepatitis b has also been called type b hepatitis, serum hepatitis, homologous serum jaundice. Deep sequencing of the hepatitis b virus in hepatocellular. An estimated 350 million people worldwide have chronic hbv infection. Nucleotide sequence of the hepatitis b virus genome subtype ayw cloned.
This is probably the first report of the hbv genome sequencing using ion torrent from india. Quantification hepatitis b virus hbv dna plays a critical role in the management of chronic hbv infections. The direct cytopathic effects of the hepatitis b virus hbv on subsequent liver damage are not fully understood in hbv infected patients. Here we use hepatitis b virus as an example to introduce a simple and efficient way for virus. Characterization of fulllength genomes of hepatitis b virus. Jun 28, 2008 by cloning and sequencing polymerase chain reaction. Complete genome sequences of seventy hbv variants obtained from fifty syrian patients sera were determined and. Hbvseq accepts usersubmitted hbv rt sequences, determines their genotypes, and compares them to the genotype consensus reference sequences. D6 hbvd6, based on the s gene sequences of isolates in papua.
Genomic analysis of hepatitis b virus and its association. The entire nucleotide sequence of genomic dna was determined for hepatitis b virus hbv of subtype ayr, which had been derived from the blood of a japanese asymptomatic carrier. Insights from deep sequencing of the hbv genomeunique, tiny. Identification of host factors that support viral replication is. Hepatitis b virus hbv has been divided into 10 genotypes, a to j, based on an 8% nucleotide sequence divergence between genotypes. Within that directory a readme file will describe the various files available. However, associations between the prevalence of various hbv genotypes and the extent of liver damage have been reported from different parts of the world. The nucleotide sequence and reading frames of a mutant hepatitis b virus subtype adr. Download the ebv hhv4 consensus genome sequence download the ebv annotated genes. They were classified as hbvb 10 strains, hbvc 9 strains, and hbvd 3 strains. See the readme file in that directory for general information about the organization of the ftp files. The hepatitis b virus hbv is a major health problem worldwide with more than 350 million people being chronic carriers. The joint position of human and hbv sequence was the breakpoints for hbv integration fig. Phylogenetic analysis of complete genome sequences of.
The specialized hepatitis b virus hbv database, hbvdb, allows the researchers to investigate the genetic variability of the virus and the viral. Coming from 46 countries and regions, these sequences were categorized as eight genotypes ah. The complete nucleotide sequence of the genome of a hepatitis b virus isolated from a naturally infected chimpanzee article pdf available in journal of general virology 69 pt 66. Fulllength hbv genome amplification, cloning and sanger sequencing. Evidence of transmission of hepatitis b virus to spouses from. Sep 10, 2018 the manuscript talks about the complete genome analysis of hepatitis b virus and represent the complete genome sequence of hbv subgenotype c2 in bangladesh. Early minion nanopore singlemolecule sequencing technology. We report the full genome sequences of seven molecular clones of hbv genotype a, amplified from an hbvinfected north indian patient.
Neolithic and medieval virus genomes reveal complex evolution of hepatitis b. The complete nucleotide sequence of hepatitis b virus genome subtype ayw cloned in escherichia coli has been determined using the maxam and gilbert method and the dideoxynucleotide method. This study is the first analysis of complete hbv genome sequences from afrocolombian population. This dataset was further supplemented with hepadnavirus isolates from chimpanzees, orangutans, and gorillas. Ono y, onda h, sasada r, igarashi k, sugino y, nishioka k. Hbv is a relaxed circular, partially doublestranded dna virus, with a unique genomic organization four overlapping reading frames encoding 7 proteins in 3. Hepatitis b virus hbv is among the most common causes of liver cirrhosis. We report the full genome sequences of seven molecular clones of hbv genotype a, amplified from an hbv infected north indian patient.
Hbv is an enveloped dna virus that replicates by reverse transcription of an rna intermediate. Fullgenome sequence analyses of hepatitis b virus hbv strains recovered from chimpanzees infected in the wild. This article is from middle east journal of digestive diseases, volume 4. In bangladesh, the rate of hbv chronicity is 26% 4, which makes it relatively higher risk than. Chronic infection is associated with an increased risk to develop severe liver diseases, including liver cirrhosis, and. The reads included concatemers of the fulllength hbv genome as illustrated in fig.
This alignment is split up into cds alignments that are optimized. The genome was 3215 nucleotides long, and differed in dna sequence by 10 from that of subtypes adw or ayw, but by only 2 90 from that of subtype adr. Illumina and nanopore methods for whole genome sequencing of. Fullgenome sequence analyses of hepatitis b virus hbv strains.
There is limited information regarding characterization and mutational analysis of hbv isolated in bangladesh. This highly annotated nucleotide sequence can be downloaded from. It was found an important presence of hbva1 and hbve. Advancing interventions to tackle the huge global burden of hepatitis b virus hbv infection depends on improved insights into virus epidemiology, transmission, withinhost diversity, drug resistance and pathogenesis, all of which can be advanced through the largescale generation of fulllength virus genome. Use text editor or plasmid mapping software to view sequence. The human papillomaviruses database collects, curates, analyzes, and publishes genetic sequences of papillomaviruses and related cellular proteins. Pdf the complete nucleotide sequence of the genome of a. The crisprcas9 system facilitates clearance of the. Dna extraction, amplification, and sequence determination and analysis. The hepatitis virus database includes hbv and provides information on.
Full length hbv dna was amplified according to the protocol described by gunther et al. The hepatitis b virus hbv hbx regulatory protein is required for hbv replication and involved in hbv related carcinogenesis. Complete genome sequence of a precoredefective hepatitis b. Hepatitis b virus hbv, a causative agent for acutechronic hepatitis and hepatocellular carcinoma hcc, has a circular partially doublestranded dna genome, is about 3.
The database contains genomic sequence data from representative viruses. At the moment 8889 distinct taxonomic names are assigned based on 11845 reference. The purpose of this study was to determine the distribution of hbv genotypes in patients with chronic. A prior to correction one fulllength read per concatemer, b concatemers corrected by consensus. Complete genome sequence and phylogenetic relatedness of. Plasmid sequence and snapgene enhanced annotations. The number of hepatitis b virus hbv whole genomic sequences in public nucleotide databases.
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